Molecular phylogeny of Sinocyclocheilus (Cypriniformes : Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocbeilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony. Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau. © 2005 Published by Elsevier Inc.

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.

Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus Sinocyclocheilus (Pisces: Cypriniformes)

The cyprinid fish genus Sinocyclocheilus, as the most cavefish rich genus, includes many species showing striking adaptation to caves and convergent reduction or even loss of eyes and pigmentation. RH1 is responsible for dim vision. In order to explore the evolution of RH1 gene in this genus, we sequenced the complete gene from 28 individuals of 16 representative species of Sinocyclocheilus, with cave and surface species included. Phylogenetic analyses supported the monophyly of Sinocyclocheilus and polyphyly of the cave species. Codon models implemented in PAML were used to infer the evolution of RH1. We found that Sinocyclocheilus had a significantly higher evolutionary rate for amino acids than other cyprinid fishes compared, which might be the result of relaxation of purifying selection and could be ascribed to cave habit of this genus. In contrast to previous hypotheses, both cave and surface lineages exhibited a similar rate of molecular evolution, so the RH1 of cave species may still be functional, although these species were highly adapted to cave environment. Two amino acid substitutions (D83G and E122V) that were not reported before were found, which may be useful for site-directed mutagenesis in the future.

水利水电岩溶发育深度的定量化理论研究

The distribution in outcrop of carbonate rocks in China is about 3.44×106km2 and accounts for over one third of the total area of the country, mainly in the Yangtze valley and the Yungui tableland ,and there is a great plenty of Water and hydropower resources in these carbonate area. A large number of projects will be built in order to develop the Water and hydropower resources. They are facing amount of complicated problems of karsts, specially the problem of the depths of karsts below water, which is a key problem that hasn’t been solved well theoretically. So, systematically research in quantitative analysis of the problem is necessary, which is very important to solve the inconsistency between current theories and facts, and is helped to foresee the depth of karsts below water and decrease the expense of the engineering. For the problem mentioned above, the thesis makes a detailed research on the length of corrosion of karsts water, based on the kinetics of corrosion, and founds the primary theory about the processes of four typical geologic elements, which are single fracture, single conduit, porous limestone and fractured limestone. And it has done a deep research upon the characterties and kinetics of corrosion of the four typical geologic elements by simulation using the programme edited by the author. The thesis also makes a discussion on the general model and process of the form of caves by using the founded theory. According to the characteristic of Water Resource and Hydropower engineering, the thesis creates three representative flow-dissolution models for three types of common geologic conditions under the induction of the theory kinetics of corrosion of karsts water. It has done quantitative research upon the process of dissolution and brought out primary theory about quantitative analysis of the depth of karsts below water as well. It found that the depth of karsts below water relates to the specific geologic conditions and the time of dissolution by simulation based on typical parameters and deep analysis of the result. That is to say there are karsts caves in any depths in flow areas of groundwater in specific geologic conditions and appropriate time. The thesis also discourses three basic problems that frequently encountered in the reconnaissance of Water Resource and Hydropower engineering, which are karsts base level, essential conditions of karsts, the comparability of caves and terrace, and indicates the importance of time in karsts. Finally, as an application, the karsts of the scheming Qianzhong water resource engineering is analyzed by the primary theory founded of quantitative analysis. The result of the application comes to a conclusion that the theory accords with the facts properly.

塔里木盆地奥陶系不整合面岩溶作用特征与油气储层研究

Based on the principle and methods of carbonate sedimentology and reservoir geology, and guided by the theories of carbonate reservoir geology, the palaeokarst of Ordovician carbonate rocks in Tarim Basin has been comprehensively studied with multiple methods from different branches of geology. It is indicated that the features and distribution of palaeokarstification have developed in Ordovician carbonates. The controlling of karstification to Ordovician carbonate reservoirs has been discussed. Regional distribution of carbonate reservoirs controlled by karstification has been predicted within this basin. The main consents and conclusions of the this dissertation is as follows: Nine key indicators to the recognition of palaeokarst are proposed in terms of careful observation upon the well cores, lithological and geochemical analyses, and drilling and logging responses to the karst caves and fractures. The time and environment of cave filling are documented from careful research of lithofacies, mineralogy, and geochemistry of the physical and chemical fillings within karst caves. The caves in Ordovician carbonates were filled in Early Carboniferous in Lunnan area. The muddy filling in upper caves was deposited under subaerial fresh-water setting, while the muddy filling in lower caves was formed in the mixed water body of fresh-water and dominated sea water. Although most chemical fillings are suggested being precipated in the burial diagenetic environment after karstification but mineralogic and geochemical characteristics of some chemical fillings indicates they formed in meteoric environment during the karstification. It is obvious that the palaeokarst has been zoned in vertical profile. It can be divided into four units from top to bottom: surface karst, vadose karst, phreatic and tranquil flow zones. Between two types of limestone karst and dolostone karst are firstly differentiated in Tarim Basin, based on the comparison of features of each karst zone in limestone and dolostone regions. In Tabei area, the lowest depth of karstification is approximately 300 m below the Upper Ordovician unconformity interface, while the bottom depth of karstification in Tazhong area ranges commonly from 300 to 400 m, in rare cases may be up to 750 m below the upper Ordovician unconformity interface. In Lunnan and Tazhong areas, the palaeokarst morphology and the surface hydrosystem are firstly reconstructed based on the top of carboniferous "Shuangfeng limestone bed (Double-Peaks limestone)" as basal. According to the palaeomorphologic feature, karst topography can be divided into three units: karst upland, karst slope, and karst valley. Vadose zone was well developed in karst upland, and it can be found in a quite depth. Both vadose and phreatic zones were well developed in karst slope and upstream valley. In downstream valley, the karstification is not strong, the vadose and phreatic zones are thin in thickness. In Tazhong and Yingmaili areas, karstification is also developed in relict carbonate palaeo-hills which existed as isolated blocks admits clastic strata.

溶蚀岩体渗透水力学特性研究

Seepage control in karstic rock masses is one of the most important problems in domestic hydroelectric engineering and mining engineering as well as traffic engineering. At present permeability assessment and leakage analysis of multi-layer karstic rock masses are mainly qualitative, while seldom quantitative. Quantitative analyses of the permeability coefficient and seepage amount are conducted in this report, which will provide a theoretical basis for the study of seepage law and seepage control treatment of karstic rocks. Based on the field measurements in the horizontal grouting galleries of seepage control curtains on the left bank of the Shuibuya Hydropower Project on the Qingjiang river, a hydraulic model is established in this report, and the computation results will provide a scientific basis for optimization of grouting curtain engineering. Following issues are addressed in the report. (1) Based on the in-situ measurements of fissures and karstic cavities in grouting galleries, the characteristics of karstic rock mass is analyzed, and a stochastic structural model of karstic rock masses is set up, which will provide the basis for calculation of the permeability and leakage amount of karstic rock mass. (2) According to the distribution of the measured joints in the grouting galleries and the stochastic results obtained from the stochastic structural model of karstic rock mass between grouting galleries, a formula for computation of permeability tensor of fracturing system is set up, and a computation program is made with Visual Basic language. The computation results will be helpful for zoning of fissured rock masses and calculation of seepage amount as well as optimization of seepage control curtains. (3) Fractal theory is used to describe quantitatively the roughness of conduit walls of karstic systems and the sinuosity of karstic conduits. It is proposed that the roughness coefficient of kastic caves can be expressed by both fractal dimension Ds and Dr that represent respectively the extension sinuosity of karstic caves and the roughness of the conduit walls. The existing formula for calculating the seepage amount of karstic conduits is revised and programmed. The seepage amount of rock masses in the measured grouting galleries is estimated under the condition that no seepage control measures are taken before reservoir impoundment, and the results will be helpful for design and construction optimization of seepage curtains of the Shuibuya hydropower project. This report is one part of the subject "Karstic hydrogeology and the structural model and seepage hydraulics of karstic rock masses", a sub-program of "Study on seepage hydraulics of multi-layer karstic rock masses and its application in seepage control curtain engineering", which is financially supported by the Hubei Provincial key science and technology programme.

工程地质三维可视化技术及其工程应用研究

Study of 3D visualization technology of engineering geology and its application to engineering is a cross subject which includes geosciences, computer, software and information technology. Being an important part of the secondary theme of National Basic Research Program of China (973 Program) whose name is Study of Multi-Scale Structure and Occurrence Environment of Complicated Geological Engineering Mass(No.2002CB412701), the dissertation involves the studies of key problems of 3D geological modeling, integrated applications of multi-format geological data, effective modeling methods of complex approximately layered geological mass as well as applications of 3D virtual reality information management technology.The main research findings are listed below:Integrated application method of multi-format geological data is proposed,which has solved the integrated application of drill holes, engineering geology plandrawings, sectional drawings and cutting drawings as well as exploratory trenchsketch. Its application can provide as more as possible fundamental data for 3Dgeological modeling.A 3D surface construction method combined Laplace interpolation points withoriginal points is proposed, so the deformation of 3D model and the crossing error ofupper and lower surface of model resulted from lack of data when constructing alaminated stratum can be eliminated.3D modeling method of approximately layered geological mass is proposed,which has solved the problems of general modeling method based on the sections or points and faces when constructing terrain and concordant strata.The 3D geological model of VII dam site of Xiangjiaba hydropower stationhas been constructed. The applications of 3D geological model to the auto-plotting ofsectional drawing and the converting of numerical analysis model are also discussed.3D virtual reality information integrated platform is developed, whose mostimportant character is that it is a software platform having the functions of 3D virtualreality flying and multi-format data management simultaneously. Therefore, theplatform can load different 3D model so as to satisfy the different engineeringdemands.The relics of Aigong Cave of Longyou Stone Caves are recovered. Thereinforcement plans of 1# and 2# cave in phoenix hill also be expressed. The intuitiveexpression provided decision makers and designers a very good environment.The basic framework and specific functions of 3D geological informationsystem are proposed.The main research findings in the dissertation have been successfully applied to some important engineering such as Xiangjiaba hydropower station, a military airport and Longyou Stone Caves etc.